That was UPN forcing the situation on the show however. Braga wanted more serialization on the show, but UPN overruled and forced the show to be episodic.
I believe that's true, but I'm talking about issues I had with the show as it actually exists, not which behind-the-scene decision maker was responsible for those problems.
Which aliens do you refer? The Kazon and the Vidians both stopped showing up after the second season, essentially. The Hirogen were established when they were introduced to have a presence that stretched out to the Alpha Quadrant, Species 8472 are from a different realm and enter our space courtesy of a vortex which can open anywhere, and we know from TNG the Borg control a vast amount of space.
I was OK with the logic of re-encountering the Vidiians, Species 8472, and the Borg (though dramatically I would argue they should have pulled back on the Borg and 8472, but continuity-wise it's fine). I could have bought two years of being in Kazon space, but repeatedly encountering the same specific Kazon over that length of time wasn't plausible to me. The others I was thinking of was the late encounters with the Hirogen and the Talaxians, and that colony of Ocampans they found.
I don't recall them setting that up for the Hirogen, but I could be forgetting. But even if they managed explanations for that and the Borg and 8472, for me the main point was the cumulative effect: we had a show about traveling in one direction, and they couldn't stop themselves from going back to these same wells again and again. Even if they got better with setting up the logic of re-encountering these species along their journey, it still read to me as a show that was fundamentally uninterested in it's own premise.
I actually thought the original Hirogen arc was a great example of an occasion Voyager did honor it's own premise -- it was an excellent idea to tangle with the same species for 5 consecutive episodes and then leave them behind. I wish they had tried that same structure another 2 or 3 times.
Which crew members did they forget were alive or dead?
I believe I've read an interview with some VOY writer/producer about how they thought either Carey, Samantha Wildman, or both had been killed off, and were surprised to learn they were still alive and could still be used. But I didn't find it in 5 minutes of poking around Memory Alpha, and I don't feel like spending more time on it. It's possible my memory is playing tricks on me. But it's definitely consistent with their strange pattern of recurring characters just vanishing, until we went back in time to the seasons where these characters had been appearing regularly, and there they are again!